RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

Searching..................................................done

Query= psy3963
         (128 letters)



>3k2k_A Putative carboxypeptidase; structural genomics, joint center
           structural genomics, JCSG, protein structure initiative;
           2.49A {Burkholderia mallei atcc 23344}
          Length = 403

 Score = 35.2 bits (80), Expect = 0.003
 Identities = 5/32 (15%), Positives = 9/32 (28%)

Query: 84  PYFYCDFHGHSLKKNIFLYGCSSQESWLSSDK 115
              + D HG      +F  G      +    +
Sbjct: 280 CDLFFDIHGDEDLPYVFAAGSEMLPGFTEQQR 311



 Score = 33.6 bits (76), Expect = 0.012
 Identities = 7/58 (12%), Positives = 17/58 (29%), Gaps = 3/58 (5%)

Query: 2   LSRLLEQCALSFDPKSSHYKIE--RSKESTARITIWREYGVVRSYTMESTYCGFDQGS 57
                ++ +  F  +  +   +        A   I   +G + S T+E  +       
Sbjct: 317 FIDSFKRASPDFQDEHGYPPGKYREDAFKLASKYIGHRFGCL-SLTLEMPFKDNANLP 373


>3l2n_A Peptidase M14, carboxypeptidase A; putative carboxypeptidase A,
           structural genomics, joint CENT structural genomics,
           JCSG; 2.39A {Shewanella denitrificans}
          Length = 395

 Score = 34.8 bits (79), Expect = 0.004
 Identities = 7/60 (11%), Positives = 19/60 (31%), Gaps = 7/60 (11%)

Query: 2   LSRLLEQCALSFDPKSSHYKIERSKESTARITIWREY----GVVRSYTMESTYCGFDQGS 57
               L   +  F    + +  ++ +   A +T+   +        S T+E  +      +
Sbjct: 308 FVAALSLASADF---QTEFGYDKDEPGKANLTVACNWVANTFKCLSNTLEMPFKDNANLA 364



 Score = 32.4 bits (73), Expect = 0.026
 Identities = 7/30 (23%), Positives = 12/30 (40%)

Query: 81  KKTPYFYCDFHGHSLKKNIFLYGCSSQESW 110
           +     + D HG      +FL GC    ++
Sbjct: 268 ETGVDLFYDVHGDEGLPYVFLAGCEGIPNY 297


>4a37_A Metallo-carboxypeptidase; metallo-protease, hydrolase; 1.60A
           {Pseudomonas aeruginosa} PDB: 4a38_A 4a39_A*
          Length = 388

 Score = 34.0 bits (77), Expect = 0.008
 Identities = 6/35 (17%), Positives = 12/35 (34%)

Query: 81  KKTPYFYCDFHGHSLKKNIFLYGCSSQESWLSSDK 115
           +     + D HG     ++F  GC     +    +
Sbjct: 263 RHGVDLFLDIHGDEEIPHVFAAGCEGNPGYTPRLE 297



 Score = 34.0 bits (77), Expect = 0.009
 Identities = 6/45 (13%), Positives = 14/45 (31%), Gaps = 4/45 (8%)

Query: 17  SSHYKIERSKESTARITIWREYGVVR----SYTMESTYCGFDQGS 57
              +   RS    A + +   +        ++T+E  +   D   
Sbjct: 314 QIRHGYPRSAPGQANLALACNFVGQTYDCLAFTIEMPFKDHDDNP 358


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
            acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
            synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
          Length = 2006

 Score = 29.2 bits (65), Expect = 0.41
 Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 35/107 (32%)

Query: 14   DPKSS--HYKIERSKESTARITIWRE-YGVVRSYTMESTYCGFDQGS--FKIGTKESMKI 68
            +P +   H+  E+ K    RI   RE Y    +   E+   G  +    FK   + S   
Sbjct: 1668 NPVNLTIHFGGEKGK----RI---RENYS---AMIFETIVDGKLKTEKIFKEINEHSTSY 1717

Query: 69   V----RGLI---EF-----------CTRVLKKTPYFYCD--FHGHSL 95
                 +GL+   +F               LK       D  F GHSL
Sbjct: 1718 TFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL 1764


>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 29.1 bits (64), Expect = 0.44
 Identities = 19/103 (18%), Positives = 31/103 (30%), Gaps = 32/103 (31%)

Query: 1   MLSRLLEQCALSFDPKSSHYKI-----ERSKESTARITIWREYGVVRSYTMESTYCGFDQ 55
           ++++L +   +   PK S   I     E   +      + R   +V  Y +  T+   D 
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS--IVDHYNIPKTFDSDD- 463

Query: 56  GSFKIGTKESMKIVRGLIEFCTRVLKKTPYFYCDFH-GHSLKK 97
                        +               YFY   H GH LK 
Sbjct: 464 --------LIPPYLDQ-------------YFY--SHIGHHLKN 483


>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
          ATP-binding, nucleotide-binding, HYD; 2.20A
          {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
          Length = 574

 Score = 28.9 bits (65), Expect = 0.49
 Identities = 4/41 (9%), Positives = 12/41 (29%)

Query: 57 SFKIGTKESMKIVRGLIEFCTRVLKKTPYFYCDFHGHSLKK 97
             +   ++ + V+         L+K  +   +  G     
Sbjct: 16 GLGLTINQAQRAVKHFGADALDRLEKDLFTLTEVEGIGFLT 56


>2y9u_A Tumor protein 63; apoptosis, sterIle alpha motif, 5-helix bundle,
          mutations, A syndrome; 1.60A {Homo sapiens} PDB: 1rg6_A
          Length = 69

 Score = 23.8 bits (51), Expect = 8.9
 Identities = 6/22 (27%), Positives = 11/22 (50%)

Query: 54 DQGSFKIGTKESMKIVRGLIEF 75
          D  S KI  +    I +G+++ 
Sbjct: 41 DLASLKIPEQFRHAIWKGILDH 62


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.323    0.136    0.421 

Gapped
Lambda     K      H
   0.267   0.0505    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,915,562
Number of extensions: 97008
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 152
Number of HSP's successfully gapped: 11
Length of query: 128
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 45
Effective length of database: 4,384,350
Effective search space: 197295750
Effective search space used: 197295750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.0 bits)